Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:20 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for SpacePAC on nebbiolo2


To the developers/maintainers of the SpacePAC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpacePAC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1917/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpacePAC 1.36.0  (landing page)
Gregory Ryslik
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/SpacePAC
git_branch: RELEASE_3_16
git_last_commit: 5818c8f
git_last_commit_date: 2022-11-01 11:08:34 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SpacePAC
Version: 1.36.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SpacePAC.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings SpacePAC_1.36.0.tar.gz
StartedAt: 2023-04-11 00:10:48 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 00:14:27 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 219.7 seconds
RetCode: 0
Status:   OK  
CheckDir: SpacePAC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SpacePAC.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings SpacePAC_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/SpacePAC.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘SpacePAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpacePAC’ version ‘1.36.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpacePAC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘iPAC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SpaceClust: no visible global function definition for ‘flush.console’
SpaceClust: no visible global function definition for ‘ppois’
create.Distance.Matrix: no visible global function definition for
  ‘dist’
create.Result.Matrix: no visible global function definition for
  ‘p.adjust’
get.Avg.Neighbor.Distance: no visible global function definition for
  ‘dist’
get.Local.Radius.Results: no visible global function definition for
  ‘sd’
make.3D.Sphere: no visible global function definition for ‘rgl.open’
make.3D.Sphere: no visible global function definition for ‘rgl.bg’
make.3D.Sphere: no visible global function definition for ‘plot3d’
make.3D.Sphere: no visible global function definition for ‘decorate3d’
make.3D.Sphere: no visible global function definition for ‘spheres3d’
Undefined global functions or variables:
  decorate3d dist flush.console p.adjust plot3d ppois rgl.bg rgl.open
  sd spheres3d
Consider adding
  importFrom("stats", "dist", "p.adjust", "ppois", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
SpaceClust 34.215  0.412  36.757
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SpacePAC.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/SpacePAC.Rcheck/00check.log’
for details.



Installation output

SpacePAC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL SpacePAC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘SpacePAC’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SpacePAC)

Tests output

SpacePAC.Rcheck/tests/runTests.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("SpacePAC")
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith


Attaching package: 'BiocGenerics'

The following object is masked from 'package:gdata':

    combine

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:gdata':

    first, first<-

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:gdata':

    trim


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00 
Processing radius # 2 : radius length = 2.00 : Percentage complete 0.25 
Processing radius # 3 : radius length = 3.00 : Percentage complete 0.50 
Processing radius # 4 : radius length = 4.00 : Percentage complete 0.75 
Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00 
Processing radius # 2 : radius length = 2.00 : Percentage complete 0.25 
Processing radius # 3 : radius length = 3.00 : Percentage complete 0.50 
Processing radius # 4 : radius length = 4.00 : Percentage complete 0.75 


RUNIT TEST PROTOCOL -- Tue Apr 11 00:13:05 2023 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SpacePAC RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 11.615   0.444  12.047 

Example timings

SpacePAC.Rcheck/SpacePAC-Ex.timings

nameusersystemelapsed
SpaceClust34.215 0.41236.757
SpacePAC-package000
make.3D.Sphere000